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Open Access Publications from the University of California

Scholarly Works (66 results)

  • Article
Recent Work (2010)

When two users transmit signals to a common receiver, one can design precoders to cancel the interference for each user, if each user knows all the channel information perfectly. Also the diversity for each user is full. However, in practice, perfect channel information is not available. In this paper, we design precoders for two users with two transmit antennas and one receiver with two receive antennas using quantized feedback. We propose to construct codebook using Grassmannian line packing. By choosing precoders from the codebook properly, our proposed scheme can cancel the interference for each user. Also we analytically prove that our system can achieve full diversity for each user. Then we extend our scheme to any number of transmit and receive antennas. Simulation results confirm our analytical proof and show that our scheme can serve as a bridge between a system with no feedback and a system with perfect feedback.

    Cover page: Multiple-Antenna Interference Cancellation and Detection for Two Users Using Quantized Feedback
    • Thesis
    • Peer Reviewed
    UC San Francisco Electronic Theses and Dissertations (2012)

    The etiologies of human primary immunodeficiencies (PIDs) often yield novel insights about the immune system. This thesis revealed an unexpected regulatory role for magnesium in the immune system from the characterization of a novel PID now named X-linked immunodeficiency with magnesium defect, Epstein Barr Virus (EBV) infection and neoplasia (XMEN) disease. This story stemmed from the characterization of two young brothers of a non-consanguineous family exhibiting recurrent viral infections and decreased thymic output of CD4+ T cells. The mother of these two boys was found to have completely skewed lyonization in her T cells, suggesting that she carried a defective X-linked gene that confers decreased fitness relative to the wildtype allele. Using X-chromosome exon capture next-generation sequencing, a 10 base pair deletion ablating a splicing junction of Magnesium Transporter 1 (MAGT1) was found by identifying genes with missing coverage in the two boys but not in the mother. This mutation led to altered splicing, frameshift, early termination, and absent protein expression. Five additional unrelated patients with deleterious mutations in MAGT1 were later identified, and they all suffered from chronic EBV infections and a propensity to develop lymphomas. MagT1 is a magnesium selective transporter required for zebrafish development that had unknown roles in human biology. We found that MagT1 mediates a transient magnesium flux required for the function of inducible T cell kinase (ITK) upon T cell antigen receptor (TCR) stimulation, implicating Mg2+ as a novel second messenger. Moreover, we also found that MagT1 deficiency leads to decreased basal free Mg2+ and downmodulation of NKG2D, a receptor mediating antiviral and antitumor cytotoxicity, and both of these defects can be restored by magnesium supplementation. These findings not only explain the disease manifestation of XMEN patients but also provide diagnostic and/or therapeutic insights for this disease and disorders requiring immunomodulation such as autoimmunity and allograft rejections.

      Cover page: XMEN disease reveals novel regulatory roles for magnesium in the immune system
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2022)
      The plant hormone salicylic acid plays an important role in balancing plant immunity and growth. In this issue of Cell Host & Microbe, Liu et al. (2022) discovered that a long non-coding RNA, lncSABC1, promotes growth in uninfected plants and unleashes defenses when pathogens attack by transcriptionally regulating salicylic acid biosynthesis.
        Cover page: LncRNA gets into the balancing act.
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2022)

        Background

        The current methodology used to detect, diagnose, and monitor many types of cancers requires invasive tissue biopsy testing. Recently, liquid biopsy using blood, plasma, urine, saliva, and various other bodily fluids has shown utility to solve many issues associated with tissue biopsy. Blood/plasma has received most of the attention within the liquid biopsy field, however, obtaining blood samples from patients is still somewhat invasive and requires trained professionals. Using urine to detect cell-free DNA cancer biomarkers offers a truly non-invasive sampling method that can be easily and reproducibly conducted by patients.

        Content

        Novel technologies and approaches have made the detection of small quantities of cell-free tumor DNA of varying lengths possible. Recent studies using urine circulating tumor DNA to detect cancer mutations and other biomarkers have shown sensitivity comparable to blood/plasma cell-free DNA liquid biopsy for many cancer types. Thus, urine cell-free DNA liquid biopsy may replace or provide supplementary information to tissue/blood biopsies. Further investigation with larger patient cohorts and standardization of pre-analytical factors is necessary to determine the utility of urine cell-free DNA liquid biopsy for cancer detection, diagnosis, and monitoring in a clinical setting.

        Summary

        In this mini-review we discuss the biological aspects of cell-free DNA in urine, numerous studies using urine cell-free DNA to detect urological cancers, and recent studies using urine cell-free DNA to detect and monitor non-urological cancers including lung, breast, colorectal, and other cancers.
          Cover page: Urinary Cell-Free DNA in Liquid Biopsy and Cancer Management
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2017)
          Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA sequencing. Therefore, the chapter is divided into two main sections regarding the type of the library constructed (small and long ncRNA libraries), from saliva collection, RNA extraction and quantification to cDNA library generation and corresponding QCs. Using these invaluable technical tools, one can identify thousands of ncRNA species in saliva. These methods indicate that salivary exRNA provides an efficient medium for biomarker discovery of oral and systemic diseases.
            Cover page: RNA Sequencing Analysis of Salivary Extracellular RNA
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2023)
            Liquid biopsy is a rapidly emerging field that involves the minimal/non-invasive assessment of signature somatic mutations through the analysis of circulating tumor DNA (ctDNA) shed by tumor cells in bodily fluids. Broadly speaking, the unmet need in liquid biopsy lung cancer detection is the lack of a multiplex platform that can detect a mutation panel of lung cancer genes using a minimum amount of sample, especially for ultra-short ctDNA (usctDNA). Here, we developed a non-PCR and non-NGS-based single-droplet-based multiplexing microsensor technology, "Electric-Field-Induced Released and Measurement (EFIRM) Liquid Biopsy" (m-eLB), for lung cancer-associated usctDNA. The m-eLB provides a multiplexable assessment of usctDNA within a single droplet of biofluid in only one well of micro-electrodes, as each electrode is coated with different probes for the ctDNA. This m-eLB prototype demonstrates accuracy for three tyrosine-kinase-inhibitor-related EGFR target sequences in synthetic nucleotides. The accuracy of the multiplexing assay has an area under the curve (AUC) of 0.98 for L858R, 0.94 for Ex19 deletion, and 0.93 for T790M. In combination, the 3 EGFR assay has an AUC of 0.97 for the multiplexing assay.
              Cover page: Single-Droplet Microsensor for Ultra-Short Circulating EFGR Mutation Detection in Lung Cancer Based on Multiplex EFIRM Liquid Biopsy
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2015)
              A method to compute the similarity between different plants is proposed, using features of a plant׳s topological structure and peripheral contour, as well as its geometry. The topological structures are described using tree graphs, and their similarity can be calculated based on the edit distance of these graphs. The peripheral contour of a plant is abstracted by its three-dimensional convex hull, which is projected in several directions. The similarity of the different projections is calculated by an algorithm to compute the similarity of two-dimensional shapes. The similarity of the geometrical detail is computed by considering the geometrical properties of different level branches. Finally the overall similarity between different plants is calculated by combining these different similarity measures. The validity of proposed method is evaluated by detailed experiments.
                Cover page: A calculation method of plant similarity giving consideration to different plant featuresCreative Commons 'BY-NC-ND' version 4.0 license
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2015)
                U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenomenon required for viability of trypanosomatid parasites. Small guide RNAs encoded mainly by the thousands of catenated minicircles contain the information for this editing. We analyzed by NGS technology the mitochondrial genomes and transcriptomes of two strains, the old lab UC strain and the recently isolated LEM125 strain. PacBio sequencing provided complete minicircle sequences which avoided the assembly problem of short reads caused by the conserved regions. Minicircles were identified by a characteristic size, the presence of three short conserved sequences, a region of inherently bent DNA and the presence of single gRNA genes at a fairly defined location. The LEM125 strain contained over 114 minicircles encoding different gRNAs and the UC strain only ~24 minicircles. Some LEM125 minicircles contained no identifiable gRNAs. Approximate copy numbers of the different minicircle classes in the network were determined by the number of PacBio CCS reads that assembled to each class. Mitochondrial RNA libraries from both strains were mapped against the minicircle and maxicircle sequences. Small RNA reads mapped to the putative gRNA genes but also to multiple regions outside the genes on both strands and large RNA reads mapped in many cases over almost the entire minicircle on both strands. These data suggest that minicircle transcription is complete and bidirectional, with 3' processing yielding the mature gRNAs. Steady state RNAs in varying abundances are derived from all maxicircle genes, including portions of the repetitive divergent region. The relative extents of editing in both strains correlated with the presence of a cascade of cognate gRNAs. These data should provide the foundation for a deeper understanding of this dynamic genetic system as well as the evolutionary variation of editing in different strains.
                  Cover page: Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae
                  • Article
                  • Peer Reviewed
                  LBL Publications (2019)
                  We previously reported MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available at https://bitbucket.org/berkeleylab/metabat .
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2007)

                    Calnuc, a Golgi calcium binding protein, plays a key role in the constitution of calcium storage. Abnormal calcium homeostasis has been linked to Alzheimer's disease (AD). Excessive production and/or accumulation of beta-amyloid (Abeta) peptides that are proteolytically derived from the beta-amyloid precursor protein (APP) have been linked to the pathogenesis of AD. APP has also been indicated to play multiple physiological functions. In this study, we demonstrate that calnuc interacts with APP through direct binding to the carboxyl-terminal region of APP, possibly in a calcium-sensitive manner. Immunofluorescence study revealed that the two proteins co-localize in the Golgi in both cultured cells and mouse brains. Over-expression of calnuc in neuroblastoma cells significantly reduces the level of endogenous APP. Conversely, down-regulation of calnuc by siRNA increases cellular levels of APP. Additionally, we show that over-expression of calnuc down-regulates the APP mRNA level and inhibits APP biosynthesis, which in turn results in a parallel reduction of APP proteolytic metabolites, sAPP, CTFs and Abeta. Furthermore, we found that the level of calnuc was significantly decreased in the brain of AD patients as compared with that of age-matched non-AD controls. Our results suggest a novel function of calnuc in modulating the levels of APP and its proteolytic metabolites, which may further affect the patho/physiological functions of APP including AD pathogenesis.

                      Cover page: Calnuc binds to Alzheimer's beta-amyloid precursor protein and affects its biogenesis.
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